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Yorodumi- PDB-4kgc: Nucleosome Core Particle Containing (ETA6-P-CYMENE)-(1, 2-ETHYLEN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kgc | ||||||
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Title | Nucleosome Core Particle Containing (ETA6-P-CYMENE)-(1, 2-ETHYLENEDIAMINE)-RUTHENIUM | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN/DNA / DNA-protein complex / nucleosome / Ruthenium agents / STRUCTURAL PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information structural constituent of chromatin / nucleosome / nucleosome assembly / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Xenopus laevis (African clawed frog) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å | ||||||
Authors | Adhireksan, Z. / Davey, C.A. | ||||||
Citation | Journal: Nat Commun / Year: 2014 Title: Ligand substitutions between ruthenium-cymene compounds can control protein versus DNA targeting and anticancer activity Authors: Adhireksan, Z. / Davey, G.E. / Campomanes, P. / Groessl, M. / Clavel, C.M. / Yu, H. / Nazarov, A.A. / Yeo, C.H. / Ang, W.H. / Droge, P. / Rothlisberger, U. / Dyson, P.J. / Davey, C.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kgc.cif.gz | 323.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kgc.ent.gz | 245.5 KB | Display | PDB format |
PDBx/mmJSON format | 4kgc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kg/4kgc ftp://data.pdbj.org/pub/pdb/validation_reports/kg/4kgc | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 4 types, 8 molecules AEBFCGDH
#1: Protein | Mass: 15421.101 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233 #2: Protein | Mass: 11394.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799 #3: Protein | Mass: 14109.436 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, LOC494591 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8 #4: Protein | Mass: 13979.291 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281 |
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-DNA chain , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 44749.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#6: DNA chain | Mass: 44740.648 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 8 molecules
#7: Chemical | ChemComp-HRU / ( #8: Chemical | #9: Chemical | ChemComp-MG / | |
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-Details
Nonpolymer details | NCP CRYSTALS WERE SOAKED WITH (ETA6-P-CYMENE)-CHLORO-(1,2-ETHYLENEDIAMINE)-RUTHENIUM(II) ...NCP CRYSTALS WERE SOAKED WITH (ETA6-P-CYMENE)-CHLORO-(1,2-ETHYLENEDI |
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Sequence details | UNINTENTIO |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.93 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.5 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 2, 2011 |
Radiation | Monochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→60.6 Å / Num. obs: 55781 |
Reflection shell | Resolution: 2.69→2.84 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→60.6 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.9 / SU B: 13.757 / SU ML: 0.295 / Cross valid method: THROUGHOUT / ESU R: 0.96 / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 84.444 Å2
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Refinement step | Cycle: LAST / Resolution: 2.69→60.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.69→2.76 Å / Total num. of bins used: 20
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